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You can either manually create that directory using the Finder, or simply make a new stencil via the File Menu -> New Resource -> New Stencil and OmniGraffle will make the proper directory for you, and then you can drag your custom stencils there.

You should really see the ~/Library/Application Support/ folder, otherwise there might be something seriously missing on your mac. The ~/ means that you should look in your user-folder. There are other Library-folders on your computer, without the Application Support-folder. There are also Library-folders with the Application Support that's missing the OmniGraffle-folder. The correct one is in your user-folder.